Missing critical page components (page title, content region wrapping, etc), no idea where to begin troubleshooting

We have run into a weird issue a few times and I have no idea how to resolve it or where to begin troubleshooting. We created an omega subtheme on our development environment and pushed it up to production. Worked great on dev, but on production, we lose some critical page components:

Basically everything after the zone-content div and before the first div contextual-links-region is just missing. All other content on the page is fine.

What could this be? I think it has to be something related to the database since refreshing production over dev causes the issue to appear in dev.